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Items: 25

1.

A direct approach to estimating false discovery rates conditional on covariates.

Boca SM, Leek JT.

PeerJ. 2018 Dec 10;6:e6035. doi: 10.7717/peerj.6035. eCollection 2018.

2.

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.

Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL; Clinical Genome Resource Somatic Working Group and Clinical Interpretation of Variants in Cancer team members.

Hum Mutat. 2018 Nov;39(11):1721-1732. doi: 10.1002/humu.23651.

3.

Opportunities and obstacles for deep learning in biology and medicine.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS.

J R Soc Interface. 2018 Apr;15(141). pii: 20170387. doi: 10.1098/rsif.2017.0387. Review.

4.

Acquired Resistance to a MET Antibody In Vivo Can Be Overcome by the MET Antibody Mixture Sym015.

Pollmann SE, Calvert VS, Rao S, Boca SM, Madhavan S, Horak ID, Kjaer A, Petricoin EF, Kragh M, Poulsen TT.

Mol Cancer Ther. 2018 Jun;17(6):1259-1270. doi: 10.1158/1535-7163.MCT-17-0787. Epub 2018 Mar 15.

5.

FWER and FDR control when testing multiple mediators.

Sampson JN, Boca SM, Moore SC, Heller R.

Bioinformatics. 2018 Jul 15;34(14):2418-2424. doi: 10.1093/bioinformatics/bty064.

6.

POPSTR: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations.

Ahn J, Conkright B, Boca SM, Madhavan S.

J Comput Biol. 2018 Apr;25(4):417-429. doi: 10.1089/cmb.2017.0127. Epub 2018 Jan 2.

7.

EGR1 regulates cellular metabolism and survival in endocrine resistant breast cancer.

Shajahan-Haq AN, Boca SM, Jin L, Bhuvaneshwar K, Gusev Y, Cheema AK, Demas DD, Raghavan KS, Michalek R, Madhavan S, Clarke R.

Oncotarget. 2017 May 30;8(57):96865-96884. doi: 10.18632/oncotarget.18292. eCollection 2017 Nov 14.

8.

Multivariate meta-analysis with an increasing number of parameters.

Boca SM, Pfeiffer RM, Sampson JN.

Biom J. 2017 May;59(3):496-510. doi: 10.1002/bimj.201600013. Epub 2017 Feb 14.

9.

Quantification and expert evaluation of evidence for chemopredictive biomarkers to personalize cancer treatment.

Rao S, Beckman RA, Riazi S, Yabar CS, Boca SM, Marshall JL, Pishvaian MJ, Brody JR, Madhavan S.

Oncotarget. 2017 Jun 6;8(23):37923-37934. doi: 10.18632/oncotarget.13544. Review.

10.

Correction: Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study.

Boca SM, Nishida M, Harris M, Rao S, Cheema AK, Gill K, Wang D, An L, Gauba R, Seol H, Morgenroth LP, Henricson E, McDonald C, Mah JK, Clemens PR, Hoffman EP, Hathout Y, Madhavan S.

PLoS One. 2016 Jul 19;11(7):e0159895. doi: 10.1371/journal.pone.0159895. eCollection 2016.

11.

A Dynamic Model for the Evolution of Protein Structure.

Tal G, Boca SM, Mittenthal J, Caetano-Anollés G.

J Mol Evol. 2016 May;82(4-5):230-43. doi: 10.1007/s00239-016-9740-1. Epub 2016 May 5.

PMID:
27146880
12.

Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study.

Boca SM, Nishida M, Harris M, Rao S, Cheema AK, Gill K, Seol H, Morgenroth LP, Henricson E, McDonald C, Mah JK, Clemens PR, Hoffman EP, Hathout Y, Madhavan S.

PLoS One. 2016 Apr 15;11(4):e0153461. doi: 10.1371/journal.pone.0153461. eCollection 2016. Erratum in: PLoS One. 2016;11(7):e0159895.

13.

Modulation of Radiation Response by the Tetrahydrobiopterin Pathway.

Pathak R, Cheema AK, Boca SM, Krager KJ, Hauer-Jensen M, Aykin-Burns N.

Antioxidants (Basel). 2015 Jan 22;4(1):68-81. doi: 10.3390/antiox4010068. Review.

14.

Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for Thirteen Cancer Types.

Sampson JN, Wheeler WA, Yeager M, Panagiotou O, Wang Z, Berndt SI, Lan Q, Abnet CC, Amundadottir LT, Figueroa JD, Landi MT, Mirabello L, Savage SA, Taylor PR, De Vivo I, McGlynn KA, Purdue MP, Rajaraman P, Adami HO, Ahlbom A, Albanes D, Amary MF, An SJ, Andersson U, Andriole G Jr, Andrulis IL, Angelucci E, Ansell SM, Arici C, Armstrong BK, Arslan AA, Austin MA, Baris D, Barkauskas DA, Bassig BA, Becker N, Benavente Y, Benhamou S, Berg C, Van Den Berg D, Bernstein L, Bertrand KA, Birmann BM, Black A, Boeing H, Boffetta P, Boutron-Ruault MC, Bracci PM, Brinton L, Brooks-Wilson AR, Bueno-de-Mesquita HB, Burdett L, Buring J, Butler MA, Cai Q, Cancel-Tassin G, Canzian F, Carrato A, Carreon T, Carta A, Chan JK, Chang ET, Chang GC, Chang IS, Chang J, Chang-Claude J, Chen CJ, Chen CY, Chen C, Chen CH, Chen C, Chen H, Chen K, Chen KY, Chen KC, Chen Y, Chen YH, Chen YS, Chen YM, Chien LH, Chirlaque MD, Choi JE, Choi YY, Chow WH, Chung CC, Clavel J, Clavel-Chapelon F, Cocco P, Colt JS, Comperat E, Conde L, Connors JM, Conti D, Cortessis VK, Cotterchio M, Cozen W, Crouch S, Crous-Bou M, Cussenot O, Davis FG, Ding T, Diver WR, Dorronsoro M, Dossus L, Duell EJ, Ennas MG, Erickson RL, Feychting M, Flanagan AM, Foretova L, Fraumeni JF Jr, Freedman ND, Beane Freeman LE, Fuchs C, Gago-Dominguez M, Gallinger S, Gao YT, Gapstur SM, Garcia-Closas M, García-Closas R, Gascoyne RD, Gastier-Foster J, Gaudet MM, Gaziano JM, Giffen C, Giles GG, Giovannucci E, Glimelius B, Goggins M, Gokgoz N, Goldstein AM, Gorlick R, Gross M, Grubb R 3rd, Gu J, Guan P, Gunter M, Guo H, Habermann TM, Haiman CA, Halai D, Hallmans G, Hassan M, Hattinger C, He Q, He X, Helzlsouer K, Henderson B, Henriksson R, Hjalgrim H, Hoffman-Bolton J, Hohensee C, Holford TR, Holly EA, Hong YC, Hoover RN, Horn-Ross PL, Hosain GM, Hosgood HD 3rd, Hsiao CF, Hu N, Hu W, Hu Z, Huang MS, Huerta JM, Hung JY, Hutchinson A, Inskip PD, Jackson RD, Jacobs EJ, Jenab M, Jeon HS, Ji BT, Jin G, Jin L, Johansen C, Johnson A, Jung YJ, Kaaks R, Kamineni A, Kane E, Kang CH, Karagas MR, Kelly RS, Khaw KT, Kim C, Kim HN, Kim JH, Kim JS, Kim YH, Kim YT, Kim YC, Kitahara CM, Klein AP, Klein RJ, Kogevinas M, Kohno T, Kolonel LN, Kooperberg C, Kricker A, Krogh V, Kunitoh H, Kurtz RC, Kweon SS, LaCroix A, Lawrence C, Lecanda F, Lee VH, Li D, Li H, Li J, Li YJ, Li Y, Liao LM, Liebow M, Lightfoot T, Lim WY, Lin CC, Lin D, Lindstrom S, Linet MS, Link BK, Liu C, Liu J, Liu L, Ljungberg B, Lloreta J, Di Lollo S, Lu D, Lund E, Malats N, Mannisto S, Le Marchand L, Marina N, Masala G, Mastrangelo G, Matsuo K, Maynadie M, McKay J, McKean-Cowdin R, Melbye M, Melin BS, Michaud DS, Mitsudomi T, Monnereau A, Montalvan R, Moore LE, Mortensen LM, Nieters A, North KE, Novak AJ, Oberg AL, Offit K, Oh IJ, Olson SH, Palli D, Pao W, Park IK, Park JY, Park KH, Patiño-Garcia A, Pavanello S, Peeters PH, Perng RP, Peters U, Petersen GM, Picci P, Pike MC, Porru S, Prescott J, Prokunina-Olsson L, Qian B, Qiao YL, Rais M, Riboli E, Riby J, Risch HA, Rizzato C, Rodabough R, Roman E, Roupret M, Ruder AM, Sanjose Sd, Scelo G, Schned A, Schumacher F, Schwartz K, Schwenn M, Scotlandi K, Seow A, Serra C, Serra M, Sesso HD, Setiawan VW, Severi G, Severson RK, Shanafelt TD, Shen H, Shen W, Shin MH, Shiraishi K, Shu XO, Siddiq A, Sierrasesúmaga L, Sihoe AD, Skibola CF, Smith A, Smith MT, Southey MC, Spinelli JJ, Staines A, Stampfer M, Stern MC, Stevens VL, Stolzenberg-Solomon RS, Su J, Su WC, Sund M, Sung JS, Sung SW, Tan W, Tang W, Tardón A, Thomas D, Thompson CA, Tinker LF, Tirabosco R, Tjønneland A, Travis RC, Trichopoulos D, Tsai FY, Tsai YH, Tucker M, Turner J, Vajdic CM, Vermeulen RC, Villano DJ, Vineis P, Virtamo J, Visvanathan K, Wactawski-Wende J, Wang C, Wang CL, Wang JC, Wang J, Wei F, Weiderpass E, Weiner GJ, Weinstein S, Wentzensen N, White E, Witzig TE, Wolpin BM, Wong MP, Wu C, Wu G, Wu J, Wu T, Wu W, Wu X, Wu YL, Wunder JS, Xiang YB, Xu J, Xu P, Yang PC, Yang TY, Ye Y, Yin Z, Yokota J, Yoon HI, Yu CJ, Yu H, Yu K, Yuan JM, Zelenetz A, Zeleniuch-Jacquotte A, Zhang XC, Zhang Y, Zhao X, Zhao Z, Zheng H, Zheng T, Zheng W, Zhou B, Zhu M, Zucca M, Boca SM, Cerhan JR, Ferri GM, Hartge P, Hsiung CA, Magnani C, Miligi L, Morton LM, Smedby KE, Teras LR, Vijai J, Wang SS, Brennan P, Caporaso NE, Hunter DJ, Kraft P, Rothman N, Silverman DT, Slager SL, Chanock SJ, Chatterjee N.

J Natl Cancer Inst. 2015 Oct 12;107(12):djv279. doi: 10.1093/jnci/djv279. Print 2015 Dec. Erratum in: J Natl Cancer Inst. 2016 Apr;108(4). pii: djw106. doi: 10.1093/jnci/djw106.

15.

Serum biomarkers of habitual coffee consumption may provide insight into the mechanism underlying the association between coffee consumption and colorectal cancer.

Guertin KA, Loftfield E, Boca SM, Sampson JN, Moore SC, Xiao Q, Huang WY, Xiong X, Freedman ND, Cross AJ, Sinha R.

Am J Clin Nutr. 2015 May;101(5):1000-11. doi: 10.3945/ajcn.114.096099. Epub 2015 Mar 11.

16.

Human metabolic correlates of body mass index.

Moore SC, Matthews CE, Sampson JN, Stolzenberg-Solomon RZ, Zheng W, Cai Q, Tan YT, Chow WH, Ji BT, Liu DK, Xiao Q, Boca SM, Leitzmann MF, Yang G, Xiang YB, Sinha R, Shu XO, Cross AJ.

Metabolomics. 2014 Apr 1;10(2):259-269.

17.

Sources of variability in metabolite measurements from urinary samples.

Xiao Q, Moore SC, Boca SM, Matthews CE, Rothman N, Stolzenberg-Solomon RZ, Sinha R, Cross AJ, Sampson JN.

PLoS One. 2014 May 1;9(5):e95749. doi: 10.1371/journal.pone.0095749. eCollection 2014.

18.

Testing multiple biological mediators simultaneously.

Boca SM, Sinha R, Cross AJ, Moore SC, Sampson JN.

Bioinformatics. 2014 Jan 15;30(2):214-20. doi: 10.1093/bioinformatics/btt633. Epub 2013 Nov 6.

19.

A decision-theory approach to interpretable set analysis for high-dimensional data.

Boca SM, Bravo HC, Caffo B, Leek JT, Parmigiani G.

Biometrics. 2013 Sep;69(3):614-23. doi: 10.1111/biom.12060. Epub 2013 Aug 2.

20.

Metabolomics in epidemiology: sources of variability in metabolite measurements and implications.

Sampson JN, Boca SM, Shu XO, Stolzenberg-Solomon RZ, Matthews CE, Hsing AW, Tan YT, Ji BT, Chow WH, Cai Q, Liu DK, Yang G, Xiang YB, Zheng W, Sinha R, Cross AJ, Moore SC.

Cancer Epidemiol Biomarkers Prev. 2013 Apr;22(4):631-40. doi: 10.1158/1055-9965.EPI-12-1109. Epub 2013 Feb 8.

21.

Mathematical properties of Fst between admixed populations and their parental source populations.

Boca SM, Rosenberg NA.

Theor Popul Biol. 2011 Nov;80(3):208-16. doi: 10.1016/j.tpb.2011.05.003. Epub 2011 May 25.

22.

The genetic landscape of the childhood cancer medulloblastoma.

Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE.

Science. 2011 Jan 28;331(6016):435-9. doi: 10.1126/science.1198056. Epub 2010 Dec 16.

23.

Patient-oriented gene set analysis for cancer mutation data.

Boca SM, Kinzler KW, Velculescu VE, Vogelstein B, Parmigiani G.

Genome Biol. 2010;11(11):R112. doi: 10.1186/gb-2010-11-11-r112. Epub 2010 Nov 23.

24.

Haplotypic background of a private allele at high frequency in the Americas.

Schroeder KB, Jakobsson M, Crawford MH, Schurr TG, Boca SM, Conrad DF, Tito RY, Osipova LP, Tarskaia LA, Zhadanov SI, Wall JD, Pritchard JK, Malhi RS, Smith DG, Rosenberg NA.

Mol Biol Evol. 2009 May;26(5):995-1016. doi: 10.1093/molbev/msp024. Epub 2009 Feb 12.

25.

The genomic landscapes of human breast and colorectal cancers.

Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B.

Science. 2007 Nov 16;318(5853):1108-13. Epub 2007 Oct 11.

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